PrecisionFDA
Truth Challenge
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Explore HG002 comparison results
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| Entry | Type | Subtype | Subset | Genotype | F-score | Recall | Precision | Frac_NA | Truth TP | Truth FN | Query TP | Query FP | FP gt | % FP ma | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
77301-77350 / 86044 show all | |||||||||||||||
| gduggal-bwafb | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 65.0432 | 50.9569 | 89.8925 | 58.2960 | 426 | 410 | 418 | 47 | 47 | 100.0000 | |
| gduggal-bwafb | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 81.8829 | 73.3939 | 92.5926 | 62.2269 | 1131 | 410 | 1825 | 146 | 139 | 95.2055 | |
| ltrigg-rtg2 | SNP | * | map_l250_m2_e1 | het | 95.8720 | 92.2112 | 99.8355 | 76.2366 | 4854 | 410 | 4854 | 8 | 1 | 12.5000 | |
| hfeng-pmm2 | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.7343 | 95.5895 | 99.9775 | 64.8179 | 8886 | 410 | 8904 | 2 | 1 | 50.0000 | |
| hfeng-pmm1 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.8143 | 97.9008 | 99.7450 | 65.3085 | 19168 | 411 | 19168 | 49 | 0 | 0.0000 | |
| hfeng-pmm1 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.8143 | 97.9008 | 99.7450 | 65.3085 | 19168 | 411 | 19168 | 49 | 0 | 0.0000 | |
| jlack-gatk | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 98.6377 | 99.1486 | 98.1322 | 75.2542 | 47860 | 411 | 47652 | 907 | 540 | 59.5369 | |
| ckim-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 96.8156 | 94.2210 | 99.5572 | 26.7488 | 6701 | 411 | 6745 | 30 | 30 | 100.0000 | |
| jli-custom | INDEL | I1_5 | * | het | 99.6300 | 99.4800 | 99.7804 | 58.4682 | 78630 | 411 | 78600 | 173 | 112 | 64.7399 | |
| gduggal-snapplat | SNP | tv | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 85.2074 | 76.7402 | 95.7746 | 76.7746 | 1356 | 411 | 1360 | 60 | 34 | 56.6667 | |
| ndellapenna-hhga | INDEL | I1_5 | * | homalt | 99.4589 | 99.3199 | 99.5983 | 51.5644 | 60017 | 411 | 60008 | 242 | 186 | 76.8595 | |
| gduggal-bwafb | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.5852 | 99.2612 | 97.9184 | 64.7490 | 55220 | 411 | 55320 | 1176 | 260 | 22.1088 | |
| gduggal-bwaplat | INDEL | D1_5 | map_l125_m2_e1 | * | 78.1152 | 64.4771 | 99.0704 | 94.2799 | 746 | 411 | 746 | 7 | 1 | 14.2857 | |
| eyeh-varpipe | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 86.1593 | 93.2312 | 80.0845 | 46.3972 | 5661 | 411 | 9663 | 2403 | 2342 | 97.4615 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 96.8082 | 94.2070 | 99.5571 | 26.7517 | 6700 | 412 | 6744 | 30 | 30 | 100.0000 | |
| dgrover-gatk | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 94.0819 | 89.2259 | 99.4969 | 40.1872 | 3412 | 412 | 3560 | 18 | 17 | 94.4444 | |
| ciseli-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 79.5334 | 83.2452 | 76.1384 | 70.7854 | 2047 | 412 | 2090 | 655 | 364 | 55.5725 | |
| cchapple-custom | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.0126 | 97.4325 | 98.5996 | 53.5616 | 15635 | 412 | 16687 | 237 | 217 | 91.5612 | |
| anovak-vg | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 97.4699 | 97.9603 | 96.9843 | 55.7493 | 19787 | 412 | 20132 | 626 | 469 | 74.9201 | |
| rpoplin-dv42 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 93.6827 | 88.3154 | 99.7447 | 41.6713 | 3114 | 412 | 3126 | 8 | 8 | 100.0000 | |
| rpoplin-dv42 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 93.6827 | 88.3154 | 99.7447 | 41.6713 | 3114 | 412 | 3126 | 8 | 8 | 100.0000 | |
| gduggal-bwaplat | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 67.5892 | 52.9680 | 93.3602 | 88.9531 | 464 | 412 | 464 | 33 | 32 | 96.9697 | |
| ghariani-varprowl | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 72.2252 | 97.0052 | 57.5294 | 65.0968 | 13345 | 412 | 13375 | 9874 | 9432 | 95.5236 | |
| ghariani-varprowl | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 72.2252 | 97.0052 | 57.5294 | 65.0968 | 13345 | 412 | 13375 | 9874 | 9432 | 95.5236 | |
| qzeng-custom | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 83.1375 | 89.8020 | 77.3938 | 60.0848 | 3628 | 412 | 8600 | 2512 | 1214 | 48.3280 | |
| ltrigg-rtg2 | SNP | tv | map_siren | * | 99.4071 | 99.1030 | 99.7130 | 49.8109 | 45518 | 412 | 45517 | 131 | 9 | 6.8702 | |
| ltrigg-rtg2 | INDEL | D1_5 | HG002compoundhet | * | 97.8414 | 96.6244 | 99.0893 | 63.2729 | 11822 | 413 | 11860 | 109 | 80 | 73.3945 | |
| ltrigg-rtg2 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 98.2211 | 97.0040 | 99.4690 | 43.1148 | 13372 | 413 | 13301 | 71 | 68 | 95.7746 | |
| qzeng-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 93.4653 | 94.4068 | 92.5425 | 38.8281 | 6971 | 413 | 14221 | 1146 | 906 | 79.0576 | |
| anovak-vg | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 52.6463 | 45.0798 | 63.2653 | 66.5529 | 339 | 413 | 372 | 216 | 150 | 69.4444 | |
| dgrover-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 97.1244 | 94.8753 | 99.4828 | 30.2426 | 7646 | 413 | 7694 | 40 | 38 | 95.0000 | |
| dgrover-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 97.1244 | 94.8753 | 99.4828 | 30.2426 | 7646 | 413 | 7694 | 40 | 38 | 95.0000 | |
| ltrigg-rtg1 | SNP | * | map_l150_m0_e0 | * | 98.1003 | 96.5675 | 99.6825 | 69.8517 | 11619 | 413 | 11615 | 37 | 15 | 40.5405 | |
| jlack-gatk | SNP | * | map_l150_m1_e0 | * | 95.4882 | 98.6507 | 92.5222 | 82.5036 | 30196 | 413 | 30190 | 2440 | 190 | 7.7869 | |
| gduggal-snapplat | INDEL | * | segdup | het | 76.3682 | 71.8281 | 81.5210 | 97.0363 | 1053 | 413 | 1147 | 260 | 13 | 5.0000 | |
| gduggal-snapvard | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 0.0000 | 0.0000 | 36.7347 | 63.4328 | 0 | 414 | 18 | 31 | 12 | 38.7097 | |
| gduggal-snapfb | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 0.0000 | 0.0000 | 0.0000 | 0 | 414 | 0 | 0 | 0 | |||
| gduggal-snapplat | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 41.2069 | 31.2292 | 60.5536 | 61.3636 | 188 | 414 | 175 | 114 | 98 | 85.9649 | |
| gduggal-snapplat | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 0.0000 | 0.0000 | 0.0000 | 0 | 414 | 0 | 0 | 0 | |||
| dgrover-gatk | INDEL | D6_15 | * | hetalt | 97.1534 | 94.9352 | 99.4777 | 33.7944 | 7760 | 414 | 7809 | 41 | 39 | 95.1220 | |
| mlin-fermikit | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 83.8710 | 72.2706 | 99.9075 | 34.6038 | 1079 | 414 | 1080 | 1 | 1 | 100.0000 | |
| anovak-vg | SNP | ti | segdup | * | 97.8325 | 97.8809 | 97.7842 | 91.7442 | 19123 | 414 | 19020 | 431 | 163 | 37.8190 | |
| ckim-dragen | SNP | * | map_l125_m1_e0 | * | 98.3997 | 99.0866 | 97.7222 | 72.8507 | 44913 | 414 | 44919 | 1047 | 117 | 11.1748 | |
| jli-custom | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.3482 | 99.1423 | 99.5550 | 73.6647 | 47857 | 414 | 47648 | 213 | 149 | 69.9531 | |
| dgrover-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 97.3211 | 96.9895 | 97.6551 | 52.0760 | 13370 | 415 | 13368 | 321 | 314 | 97.8193 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | * | 73.3614 | 64.8603 | 84.4271 | 38.2979 | 766 | 415 | 759 | 140 | 137 | 97.8571 | |
| ltrigg-rtg1 | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 97.7777 | 96.0123 | 99.6093 | 42.4195 | 9992 | 415 | 9942 | 39 | 16 | 41.0256 | |
| jli-custom | SNP | * | map_l125_m1_e0 | * | 99.3178 | 99.0844 | 99.5522 | 66.7512 | 44912 | 415 | 44909 | 202 | 67 | 33.1683 | |
| jmaeng-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 96.5651 | 93.9933 | 99.2815 | 52.4049 | 6494 | 415 | 6494 | 47 | 42 | 89.3617 | |
| jmaeng-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.9588 | 99.0919 | 98.8260 | 75.8275 | 45287 | 415 | 45287 | 538 | 41 | 7.6208 | |